我喜欢在食堂吃饭。

我喜欢在食堂吃饭， as opposed to 我喜欢在家吃饭。Your point is the place you like eating in. 我在食堂喜欢吃饭（rarely heard），as opposed to 我在食堂喜欢踢足球。 Your point is the thing you like doing in the canteen.

吃饭 means have meal including, dinner/breakfast/lunch. 我喜欢在食堂吃饭: means I like to have meal in canteen much more than in other place. 我在食堂喜欢吃饭: means In canteen, I like to have meal much more than to do other things. Beacause, canteen is mainly for having meal, so this sentence means nothing.